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by-display Standard display formats and conversational patterns for BY output. Use this skill when: (1) Presenting campaign status, progress, or results, (2) Formatting screening reports, (3) Displaying error messages or checkpoints, (4) Presenting research findings or target lookups, (5) Showing long-running job progress.
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Master orchestration skill for the BY protein design agent. Use this skill when: (1) Starting any new protein or antibody design project, (2) Deciding which BY tool to use for a given task, (3) Planning a design campaign end-to-end, (4) Understanding the standard pipeline stages, (5) Setting quality thresholds and acceptance criteria, (6) Determining when to accept vs re-run designs.
For detailed scoring guidance, use by-scoring. For screening specifics, use by-screening. For epitope/hotspot analysis, use by-epitope-analysis. For campaign planning and state management, use by-campaign-manager. For database queries (PDB, UniProt, SAbDab), use by-database.
Related occupations SOC
Based on SOC occupation classification
name by-display description Standard display formats and conversational patterns for BY output. Use this skill when: (1) Presenting campaign status, progress, or results, (2) Formatting screening reports, (3) Displaying error messages or checkpoints, (4) Presenting research findings or target lookups, (5) Showing long-running job progress.
category display tags ["display","formatting","output","patterns","conversational"]
BY Display Patterns
Use these standard display formats for all campaign output. They use Unicode
box-drawing characters and markdown that render natively in Claude Code's terminal.
Never use ANSI escape codes in response text.
Status Symbols
✓ Complete / Passed / Verified
✗ Failed / Missing / Blocked
◆ In Progress / Active
○ Pending
⚠ Warning
Campaign Status Banner
Use for /by:status and phase transitions.
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
BY ► CAMPAIGN: {campaign_name}
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
| Phase | Status | Time | Details |
|----------|------------|--------|----------------------|
| Research | ✓ Complete | 45s | 3 PDB, 12 prior art |
| Plan | ✓ Complete | 30s | Preview tier, 10 VHH |
| Design | ◆ Active | 1m 15s | 5/10 designs |
| Screen | ○ Pending | — | |
| Rank | ○ Pending | — | |
Progress During Design Use for /by:watch and mid-pipeline updates.
BY ► DESIGNING ████████░░ 80% (8/10 designs)
Provider: Tamarind Bio (free tier, 7/10 jobs remaining)
Tool: BoltzGen | Protocol: nanobody-anything
Scaffold: caplacizumab | Budget: 10
Progress bar: 10 blocks total. █ (U+2588) for filled, ░ (U+2591) for empty.
Fill proportionally to percent complete.
Ranked Results Table Use for /by:results and final campaign output.
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
BY ► RESULTS: {campaign_name} — {N} candidates ranked
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
# Design Composite ipSAE ipTM pLDDT Liabilities Verdict
─── ──────────── ────────── ─────── ────── ────── ───────────── ──────────
1 design_ 003 0.871 0.85 0.82 91.2 0 crit ✓ LAB-READY
2 design_007 0.823 0.80 0.79 88.5 1 warn ✓ LAB-READY
3 design_ 001 0.756 0.72 0.75 85.1 0 crit ◆ FOLLOW-UP
4 design_012 0.534 0.45 0.62 78.3 2 crit ✗ NOT VIABLE
## Score Context
ipSAE 0.85 ████████░░ EXCELLENT (top 5% of approved therapeutics)
ipTM 0.82 ████████░░ STRONG (confident interface prediction)
pLDDT 91.2 █████████░ VERY HIGH (reliable fold prediction)
## Summary
✓ 2 lab-ready candidates | ◆ 1 needs follow-up | ✗ 1 not viable
## Next Steps
1. Submit top 2 to Adaptyv Bio ($119-215/design)
2. Run follow-up campaign with increased budget for design_ 001
3. Consider alternative epitope for design_012
Screening Battery Display Use for /by:screen and per-design screening reports.
BY ► SCREENING {design_id}
Liabilities:
✓ Deamidation 0 sites
✓ Isomerization 0 sites
✓ Oxidation 0 sites (no exposed Met)
✓ Free Cys 0 unpaired
✓ Glycosylation 0 NXS/T motifs
Developability:
Charge pH 7.4 +2.1 ✓ normal range
Hydrophobic 34% ✓ below 45% threshold
CDR3 length 12 aa ✓ within range
Structure:
ipSAE 0.85 ████████░░ EXCELLENT
ipTM 0.82 ████████░░ STRONG
pLDDT 91.2 █████████░ VERY HIGH
RMSD 1.2A ██░░░░░░░░ GOOD
VERDICT: ✓ PASS — composite score 0.871
Score Bar Format For any metric on a 0-1 scale (or 0-100 normalized to 0-1):
{metric} {value} {bar} {label}
Where bar = 10 blocks, filled proportionally: ████████░░ for 0.80.
Scale: each █ represents 10%. Round to nearest block. Examples:
0.85 = ████████░░ (8.5 rounds to 9, but display 8 for conservatism below 0.9)
0.92 = █████████░
0.50 = █████░░░░░
0.12 = █░░░░░░░░░
For pLDDT (0-100 scale), divide by 100 first: pLDDT 91.2 = 0.912 = █████████░.
Error Display Use for warnings, quota exhaustion, and failures.
╔══════════════════════════════════════════════════════╗
║ ⚠ {Error title} ║
╠══════════════════════════════════════════════════════╣
║ ║
║ {Details and alternatives} ║
║ ║
╚══════════════════════════════════════════════════════╝
Checkpoint / Safety Gate Use for lab submission gates and user approval points.
╔══════════════════════════════════════════════════════╗
║ CHECKPOINT: {Type} ║
╚══════════════════════════════════════════════════════╝
{Content — candidates table, cost estimate, safety gate status}
──────────────────────────────────────────────────────
→ {ACTION PROMPT}
──────────────────────────────────────────────────────
Next Up Block Always show at the end of major phase completions.
──────────────────────────────────────────────────────
## ▶ Next Up
**{Action}** — {description}
`/by:{command}`
<sub > `/clear` first → fresh context window</sub >
Long-Running Job Display Use for SSH remote jobs and Tamarind cloud jobs that take minutes to hours.
Fire-and-Forget Pattern For jobs submitted to remote compute:
BY ► JOB SUBMITTED
Job ID: tmr_abc123
Provider: Tamarind Bio (free tier)
Tool: BoltzGen | Protocol: nanobody-anything
Submitted: 2026-03-25 14:32 UTC
Est. time: ~45 min
Track: /by:watch tmr_ abc123
Check: /by:status
SSH Remote Job BY ► REMOTE JOB
Host: gpu-node.example.com
PID: 12345
Tool: Protenix refolding (20 seeds)
Started: 2026-03-25 14:32 UTC
Output: ~/campaigns/anti-HER2/run_001/protenix_ out/
Monitor: ssh gpu-node "tail -f ~/campaigns/.../protenix.log"
Batch Progress When monitoring a batch of jobs:
BY ► BATCH PROGRESS
████████░░ 80% (8/10 jobs complete)
✓ job_001 design_ 001 ipTM 0.82 ipSAE 0.79
✓ job_002 design_ 002 ipTM 0.75 ipSAE 0.71
✓ job_003 design_ 003 ipTM 0.88 ipSAE 0.85
...
◆ job_009 design_ 009 running (est. 5 min)
○ job_010 design_ 010 queued
Inline Progress Updates (preferred over repeated tables) Claude Code output is append-only — tables cannot be updated in place.
Instead, show one-line status updates as each phase completes. Print the
full summary table only ONCE at the end.
◆ Structure: querying PDB...
✓ Structure: 10 PDB hits, best 3DPL at 2.6Å (12s)
✓ Sequence: P62877, 108 aa, RING domain (8s)
✓ Prior Art: 0 known binders in SAbDab (15s)
✓ Epitope: 2 druggable surfaces identified (18s)
◆ Synthesizer: compiling report...
✓ Synthesizer: druggability 0.89, de novo recommended (5s)
◆ Design: submitting 1,000 designs to local GPU...
Do NOT reprint the full phase table after every step — it clutters the chat.
Use the one-line ✓/◆/✗ format between phases.
Live Progress from Compute Tools BoltzGen and Protenix output their own progress bars when run via Bash.
Claude Code streams Bash output in real-time, so users see live progress:
[Step 1/5] design - Predicting DataLoader 0: : 50%|█████ | 5/10 [00:32<00:32, 0.15it/s]
IMPORTANT: For live progress to work, the design agent MUST run compute
tools via the Bash tool (not MCP). MCP tools return results only after
completion — no streaming. Bash streams output as it happens.
Pattern for the design agent:
/home/user/.conda/envs/bg/bin/boltzgen run design_spec.yaml \
--output ./campaign_output \
--num_designs 10 \
--protocol nanobody-anything \
--budget 10
The 5-stage BoltzGen pipeline shows live progress for each step:
design — backbone generation with diffusion progress barinverse_folding — sequence design progress barfolding — Protenix refolding progress baranalysis — metrics computationfiltering — ranking and output
Pipeline Summary Table (show ONCE at end) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
BY ► CAMPAIGN COMPLETE: {target}
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
| Phase | Status | Time | Details |
|-------------|------------|--------|----------------------------------|
| Structure | ✓ Complete | 12s | 10 PDB hits, best 3DPL at 2.6Å |
| Sequence | ✓ Complete | 8s | P62877, 108 aa, RING domain |
| Prior Art | ✓ Complete | 15s | 0 known binders |
| Epitope | ✓ Complete | 18s | 2 druggable surfaces |
| Synthesizer | ✓ Complete | 5s | Druggability 0.89 |
| Design | ✓ Complete | 5m 20s | 1,000 designs, local GPU |
| Screen | ✓ Complete | 45s | 847 pass, 153 fail |
| Verify | ✓ Complete | 10s | 10 candidates verified |
Total: 7m 13s | Provider: Local GPU (RTX 6000)
Conversational Patterns
Target Lookup Formatted table with Name, UniProt ID, PDB entries, Organism, Length, Function,
followed by a recommendation and confirmation prompt.
Interface Analysis Residue table with classifications (hotspot, contact, peripheral), followed by
hotspot list and numbered options for epitope selection.
Design Launch Parameter table (modality, scaffold, budget, provider, protocol), followed by
monitoring hints (/by:watch, /by:status).
Results Ranked table (Rank, Design, ipTM, ipSAE, Liabilities, Status), followed by
Score Context bars, Summary line, and Next Steps.
Anti-Patterns
Never use ANSI escape codes in response text (they render as literal characters)
Never vary banner widths (always use the same ━ line length)
Always use BY ► prefix in banners (not GSD ► or any other prefix)
Never use random emoji -- stick to the status symbols above (✓ ✗ ◆ ○ ⚠)
Never skip the Next Up block after phase completions
Never show raw JSON from MCP tool responses -- always parse and present clean summaries
Never expose API key values in any display
